The evolution of eutrophication (i.e., phytoplankton biomass) during recent decades was examined in the coastal waters of Vilaine Bay (VB, France) in relation to those in their main external nutrient sources, the Loire and Vilaine Rivers. Dynamic Linear Models, corroborated by the Mann-Kendall test, were used to study long-term trends and seasonality of dissolved inorganic nutrient and chlorophyll a concentrations (Chl a ) in rivers and coastal waters between 1980 and 2013. The reduction in dissolved riverine inorganic phosphorus concentrations (DIP) from the early 1990s led to the decrease in their Chl a levels. However, dissolved inorganic nitrogen concentrations (DIN) decreased only slightly in the Vilaine and actually increased in the Loire, especially during summer. Simultaneously, phytoplankton in the VB has undergone profound changes with: (1) increase in biomass, (2) change in the position of the annual peak from spring to summer, and (3) increase in diatom:dinoflagellate ratios, especially in summer. The increase in phytoplankton biomass in VB, particularly in summer, was probably due to increased DIN loads from the Loire, sustained by internal regeneration of DIP and dissolved silicate from sediments. This long-term ecosystem-scale analysis reports the consequence of nutrient management scenarios focused solely on P reduction. Freshwater ecosystems upstream reveal successful recoveries through the control of P alone, while eutrophication continues to increase downstream, especially during the period of N limitation. Therefore, nutrient management strategies, paying particular attention to diffuse N-sources, are required to control eutrophication in receiving coastal waters.